6ISK

SnoaL-like cyclase XimE

• PDB DOI: https://doi.org/10.2210/pdb6ISK/pdb

• Classification: LYASE
• Organism(s): Streptomyces xiamenensis 318
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-16 Released: 2019-11-20 
• Deposition Author(s): He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.242 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis

He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.

(2019) ACS Catal 9: 5391-5399

• DOI: https://doi.org/10.1021/acscatal.9b01034

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.78 kDa 
• Atom Count: 1,935 
• Modelled Residue Count: 240 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XimE, SnoaL-like domain protein	A, B	158	Streptomyces xiamenensis 318	Mutation(s): 0  Gene Names: ximE EC: 4.2.99
UniProt
Find proteins for U5Q2N8 (Streptomyces xiamenensis) Explore U5Q2N8  Go to UniProtKB:  U5Q2N8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.242 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.894	α = 90
b = 79.894	β = 90
c = 111.721	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81473105

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references